I think it's probably impossible to completely mod the weapon effects, because so many improvised weapons are not listed, and there's no distinction in the mod data for throwing, but throwing seems to be much more powerful than using something as a hand weapon (which I guess is a code bug rather than a damage data problem).
However, I gave it a shot, figuring I could just not throw things, and the AI probably wouldn't either. So I made a few tweaks, added a few weapons and armor entries, and changed the arrows and bolts for example form damage:100 to damage:15 and damage:10 respectively, reloaded the game and returned to the place where my entire elite party with shields and armor had just been massacred by a couple of goblins with bows before they could close the range by more than a few steps. Returning with my new party, we made it through the open ground and my new sword/chain/shield dwarf was just rounding a corner when he was shot through the major organs and mortally wounded by the first arrow that hit him, from a goblin some distance away in the dark. Not dead yet, I had him throw the spare warhammer he had in his backpack (what, no delay to do something with my sword and get a warhammer out of a backpack and throw it, and then get my sword back in hand???). My swordsdwarf has no skill in throwing at all, but I'm peeved, so I target the eyes in the dark and WHAM! Goblin smashed, he crumples to the ground immediately. Ok, well that was satisfying! Seemed awfully easy though. I guess the hit was lucky.
It seems like the modded arrow damage has no noticeable effect on the lethality of arrows, though. I see that reloading the game does seem to have "recompiled" the RAW data, but does it not really have an effect on the equipment in the game in progress until I recreate a new world?
Or is it just that there is a bug where anything thrown is extremely deadly no matter what the mod data is set to?